8UMG | pdb_00008umg

Chromodomains of human CHD1 complexed with UNC10142

• PDB DOI: https://doi.org/10.2210/pdb8UMG/pdb

• Classification: PEPTIDE BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
• Mutation(s): Yes 


• Deposited: 2023-10-17 Released: 2024-10-23 
• Deposition Author(s): Graboski, A.L., Redinbo, M.R.
• Funding Organization(s): National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA), National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.320 (Depositor), 0.309 (DCC) 
• R-Value Work: 
  0.238 (Depositor), 0.226 (DCC) 
• R-Value Observed: 
  0.246 (Depositor) 

Starting Model: experimental

Literature

Optimization of a quinazoline-based scaffold against human CHD1

Johnson, R.L., Graboski, A.L., Walton, W.G., James, L.I., Redinbo, M.R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by (software)

Macromolecule Content 

• Total Structure Weight: 67.67 kDa 
• Atom Count: 3,635 
• Modeled Residue Count: 437 
• Deposited Residue Count: 561 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Chromodomain-helicase-DNA-binding protein 1	A, B, C	187	Homo sapiens	Mutation(s): 2  Gene Names: CHD1 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for O14646 (Homo sapiens) Explore O14646  Go to UniProtKB:  O14646
PHAROS:  O14646 GTEx:  ENSG00000153922

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X31 (Subject of Investigation/LOI)	D [auth A], E [auth B]	1-{4-[{2-(azonan-1-yl)-6-methoxy-7-[3-(piperidin-1-yl)propoxy]quinazolin-4-yl}(methyl)amino]piperidin-1-yl}ethan-1-one C33 H52 N6 O3 PHKQQZUOUUSBQB-UHFFFAOYSA-N
CL (Subject of Investigation/LOI)	F [auth B], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.320 (Depositor), 0.309 (DCC) 
• R-Value Work:  0.238 (Depositor), 0.226 (DCC) 
• R-Value Observed: 0.246 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.531	α = 90
b = 55.193	β = 112.779
c = 101.095	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Coot	model building
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-10-23 
Deposition Author(s): Graboski, A.L., Redinbo, M.R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)	United States	5R33DA047023-05
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	5R33DA047023-05

Revision History  

• Version 1.0: 2024-10-23
  Type: Initial release